Contacts of the strand formed by residues 181 - 187 (chain B) in PDB entry 1AOX


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with GLN 181 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  ILE      2.9     7.0    +      -       -      +
    145B  ASP*     3.2    19.6    -      -       -      +
    146B  VAL      2.8    25.8    +      -       -      -
    175B  ILE*     5.3     2.2    -      -       +      -
    176B  GLY      4.0     7.2    -      -       -      +
    177B  PRO*     4.1    18.5    -      -       +      +
    180B  THR*     1.3    78.3    -      -       -      +
    182B  VAL*     1.3    63.8    +      -       -      +
    197B  LEU*     3.4    29.3    +      -       +      +
    198B  ASN*     4.1    17.2    -      -       -      +
    200B  TYR      5.7     3.9    +      -       -      +
    206B  MET*     5.4     0.4    -      -       -      -
    240B  GLY      2.9    23.6    +      -       -      +
    242B  ARG*     3.4    26.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146B  VAL*     3.2    12.8    -      -       +      +
    148B  VAL*     4.5    13.9    -      -       +      -
    169B  PHE*     5.2     2.7    -      -       +      -
    170B  VAL*     4.7     9.9    -      -       +      -
    173B  LEU*     4.1    18.2    -      -       +      -
    175B  ILE*     3.9    24.0    -      -       +      -
    180B  THR*     4.2     2.5    -      -       +      -
    181B  GLN*     1.3    81.5    -      -       -      +
    183B  GLY*     1.3    72.7    +      -       -      +
    184B  LEU*     5.6     0.7    -      -       +      -
    195B  PHE*     3.2    21.5    -      -       +      -
    196B  ASN      3.5    11.1    -      -       -      +
    197B  LEU*     3.7     7.0    +      -       -      -
    206B  MET*     3.7    30.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146B  VAL      2.8    10.1    +      -       -      +
    147B  VAL*     4.2    10.8    -      -       -      -
    148B  VAL*     2.9    26.0    +      -       -      +
    182B  VAL*     1.3    81.2    -      -       -      +
    184B  LEU*     1.3    60.5    +      -       -      +
    185B  ILE      4.3     0.4    -      -       -      -
    195B  PHE*     3.6    12.8    -      -       -      -
    196B  ASN*     4.4     0.2    -      -       -      -
    197B  LEU*     3.7    17.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  VAL*     3.7    28.0    -      -       +      +
    150B  CYS*     4.3    10.5    -      -       +      -
    166B  LEU*     4.1    22.7    -      -       +      -
    182B  VAL*     5.6     0.9    -      -       +      -
    183B  GLY*     1.3    74.6    -      -       -      +
    185B  ILE*     1.3    72.6    -      -       -      +
    186B  GLN*     3.7    20.4    -      -       -      +
    193B  VAL      3.8     0.2    -      -       -      -
    194B  VAL*     2.8    39.8    +      -       +      -
    195B  PHE*     2.9    50.5    +      -       +      +
    210B  THR*     5.0     4.0    -      -       -      +
    213B  THR*     4.1    11.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  VAL*     4.2     6.1    -      -       +      -
    148B  VAL      2.9    12.1    +      -       -      +
    149B  VAL*     3.4    15.4    -      -       +      -
    150B  CYS*     2.8    25.3    +      -       -      -
    183B  GLY      4.3     0.2    -      -       -      -
    184B  LEU*     1.3    81.1    -      -       -      +
    186B  GLN*     1.3    74.3    +      -       -      +
    187B  TYR*     4.9     1.1    -      -       +      -
    191B  PRO*     4.2    12.1    -      -       +      -
    192B  ARG      3.4    15.3    -      -       -      +
    193B  VAL*     4.2    17.7    -      -       +      -
    195B  PHE      5.6     0.4    -      -       -      +
    226B  ALA*     5.1     2.7    -      -       +      +
    229B  TYR*     3.8    25.8    -      -       +      -
    230B  ALA*     4.0    15.0    -      -       +      +
    234B  ALA*     4.0    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  CYS*     3.0    21.5    -      -       +      +
    152B  GLU*     2.9    29.6    +      -       -      +
    159B  TRP*     3.4    23.6    -      -       +      -
    166B  LEU*     5.2     1.1    -      -       -      +
    184B  LEU*     3.7    11.8    -      -       +      +
    185B  ILE*     1.3    77.6    -      -       -      +
    187B  TYR*     1.3    63.9    +      -       -      +
    191B  PRO*     3.6     0.3    -      -       -      +
    192B  ARG*     2.7    40.1    +      -       -      +
    194B  VAL*     3.6    18.9    -      -       +      +
    213B  THR*     2.5    25.1    +      -       -      +
    214B  SER      2.8    28.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  VAL*     3.7    28.9    -      -       +      -
    150B  CYS      2.9    16.4    +      -       -      -
    151B  ASP*     3.3    28.8    -      -       +      +
    152B  GLU*     2.9    30.8    +      -       -      +
    185B  ILE*     4.9     0.9    -      -       +      -
    186B  GLN*     1.3    77.5    -      -       -      +
    188B  ALA*     1.3    69.8    +      -       -      +
    190B  ASN      3.3    14.1    -      -       -      +
    191B  PRO*     3.7    10.8    -      -       +      -
    221B  THR*     4.1    11.2    -      -       +      -
    222B  ASN      3.7    15.5    -      -       -      -
    223B  THR*     2.9    45.3    +      -       +      +
    226B  ALA*     3.5     9.2    -      -       +      -
    251B  VAL*     4.7     2.0    -      -       +      +
    252B  VAL      4.3     1.3    -      -       -      -
    253B  THR*     3.0    26.9    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il